{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9126DKWW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9126DKWW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-BinC_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM1488CZUU](/in-vitro-systems/IGVFSM1488CZUU/) has in progress subobject construct library set [IGVFDS2374NXLW](/construct-library-sets/IGVFDS2374NXLW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM1488CZUU/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9126DKWW](/measurement-sets/IGVFDS9126DKWW/) has in progress subobject auxiliary set [IGVFDS0925RKIM](/auxiliary-sets/IGVFDS0925RKIM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9126DKWW/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0925RKIM](/auxiliary-sets/IGVFDS0925RKIM/) has sequence file(s): [IGVFFI4688NGNU](/sequence-files/IGVFFI4688NGNU/), [IGVFFI7936ZYCP](/sequence-files/IGVFFI7936ZYCP/), [IGVFFI8114PNBO](/sequence-files/IGVFFI8114PNBO/), [IGVFFI8286VIOO](/sequence-files/IGVFFI8286VIOO/), [IGVFFI2580HYWK](/sequence-files/IGVFFI2580HYWK/), [IGVFFI7318XXJP](/sequence-files/IGVFFI7318XXJP/), [IGVFFI6314AXIQ](/sequence-files/IGVFFI6314AXIQ/), [IGVFFI9662YHWJ](/sequence-files/IGVFFI9662YHWJ/), [IGVFFI2363WZZB](/sequence-files/IGVFFI2363WZZB/), [IGVFFI4942LUEV](/sequence-files/IGVFFI4942LUEV/), [IGVFFI5894XEVD](/sequence-files/IGVFFI5894XEVD/), [IGVFFI7205HPYL](/sequence-files/IGVFFI7205HPYL/), [IGVFFI6815SVWK](/sequence-files/IGVFFI6815SVWK/), [IGVFFI0563VEXH](/sequence-files/IGVFFI0563VEXH/), [IGVFFI3078NRBR](/sequence-files/IGVFFI3078NRBR/), [IGVFFI7326LCAT](/sequence-files/IGVFFI7326LCAT/), [IGVFFI7906BTLR](/sequence-files/IGVFFI7906BTLR/), [IGVFFI7592LXAT](/sequence-files/IGVFFI7592LXAT/), [IGVFFI8689KTIE](/sequence-files/IGVFFI8689KTIE/), [IGVFFI8035NMOJ](/sequence-files/IGVFFI8035NMOJ/), [IGVFFI1659UYGZ](/sequence-files/IGVFFI1659UYGZ/), [IGVFFI0295UQYX](/sequence-files/IGVFFI0295UQYX/), [IGVFFI2795CFUT](/sequence-files/IGVFFI2795CFUT/), [IGVFFI0722LYVA](/sequence-files/IGVFFI0722LYVA/), [IGVFFI8114SXIX](/sequence-files/IGVFFI8114SXIX/), [IGVFFI7303UDJH](/sequence-files/IGVFFI7303UDJH/), [IGVFFI5592BNTX](/sequence-files/IGVFFI5592BNTX/), [IGVFFI9807GRVB](/sequence-files/IGVFFI9807GRVB/), [IGVFFI5000CVQY](/sequence-files/IGVFFI5000CVQY/), [IGVFFI9903IIJQ](/sequence-files/IGVFFI9903IIJQ/), [IGVFFI6541PUGX](/sequence-files/IGVFFI6541PUGX/), [IGVFFI7241SEXZ](/sequence-files/IGVFFI7241SEXZ/), [IGVFFI1054LOMD](/sequence-files/IGVFFI1054LOMD/), [IGVFFI0842KHTY](/sequence-files/IGVFFI0842KHTY/), [IGVFFI9587BSPL](/sequence-files/IGVFFI9587BSPL/), [IGVFFI8627RIAN](/sequence-files/IGVFFI8627RIAN/), [IGVFFI9442PKBX](/sequence-files/IGVFFI9442PKBX/), [IGVFFI7172AMPH](/sequence-files/IGVFFI7172AMPH/), [IGVFFI9098EJGL](/sequence-files/IGVFFI9098EJGL/), [IGVFFI9160JPFJ](/sequence-files/IGVFFI9160JPFJ/), [IGVFFI7922MDZC](/sequence-files/IGVFFI7922MDZC/), [IGVFFI0612CNEB](/sequence-files/IGVFFI0612CNEB/), [IGVFFI7354VXKL](/sequence-files/IGVFFI7354VXKL/), [IGVFFI1578XZVS](/sequence-files/IGVFFI1578XZVS/), [IGVFFI7331MKFX](/sequence-files/IGVFFI7331MKFX/), [IGVFFI5598LNFE](/sequence-files/IGVFFI5598LNFE/), [IGVFFI5961PXUV](/sequence-files/IGVFFI5961PXUV/), [IGVFFI3011PPJO](/sequence-files/IGVFFI3011PPJO/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS0925RKIM/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9126DKWW](/measurement-sets/IGVFDS9126DKWW/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS9126DKWW/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0925RKIM](/auxiliary-sets/IGVFDS0925RKIM/) has sequence file(s) [IGVFFI4688NGNU](/sequence-files/IGVFFI4688NGNU/), [IGVFFI7936ZYCP](/sequence-files/IGVFFI7936ZYCP/), [IGVFFI8114PNBO](/sequence-files/IGVFFI8114PNBO/), [IGVFFI8286VIOO](/sequence-files/IGVFFI8286VIOO/), [IGVFFI2580HYWK](/sequence-files/IGVFFI2580HYWK/), [IGVFFI7318XXJP](/sequence-files/IGVFFI7318XXJP/), [IGVFFI6314AXIQ](/sequence-files/IGVFFI6314AXIQ/), [IGVFFI9662YHWJ](/sequence-files/IGVFFI9662YHWJ/), [IGVFFI2363WZZB](/sequence-files/IGVFFI2363WZZB/), [IGVFFI4942LUEV](/sequence-files/IGVFFI4942LUEV/), [IGVFFI5894XEVD](/sequence-files/IGVFFI5894XEVD/), [IGVFFI7205HPYL](/sequence-files/IGVFFI7205HPYL/), [IGVFFI6815SVWK](/sequence-files/IGVFFI6815SVWK/), [IGVFFI0563VEXH](/sequence-files/IGVFFI0563VEXH/), [IGVFFI3078NRBR](/sequence-files/IGVFFI3078NRBR/), [IGVFFI7326LCAT](/sequence-files/IGVFFI7326LCAT/), [IGVFFI7906BTLR](/sequence-files/IGVFFI7906BTLR/), [IGVFFI7592LXAT](/sequence-files/IGVFFI7592LXAT/), [IGVFFI8689KTIE](/sequence-files/IGVFFI8689KTIE/), [IGVFFI8035NMOJ](/sequence-files/IGVFFI8035NMOJ/), [IGVFFI1659UYGZ](/sequence-files/IGVFFI1659UYGZ/), [IGVFFI0295UQYX](/sequence-files/IGVFFI0295UQYX/), [IGVFFI2795CFUT](/sequence-files/IGVFFI2795CFUT/), [IGVFFI0722LYVA](/sequence-files/IGVFFI0722LYVA/), [IGVFFI8114SXIX](/sequence-files/IGVFFI8114SXIX/), [IGVFFI7303UDJH](/sequence-files/IGVFFI7303UDJH/), [IGVFFI5592BNTX](/sequence-files/IGVFFI5592BNTX/), [IGVFFI9807GRVB](/sequence-files/IGVFFI9807GRVB/), [IGVFFI5000CVQY](/sequence-files/IGVFFI5000CVQY/), [IGVFFI9903IIJQ](/sequence-files/IGVFFI9903IIJQ/), [IGVFFI6541PUGX](/sequence-files/IGVFFI6541PUGX/), [IGVFFI7241SEXZ](/sequence-files/IGVFFI7241SEXZ/), [IGVFFI1054LOMD](/sequence-files/IGVFFI1054LOMD/), [IGVFFI0842KHTY](/sequence-files/IGVFFI0842KHTY/), [IGVFFI9587BSPL](/sequence-files/IGVFFI9587BSPL/), [IGVFFI8627RIAN](/sequence-files/IGVFFI8627RIAN/), [IGVFFI9442PKBX](/sequence-files/IGVFFI9442PKBX/), [IGVFFI7172AMPH](/sequence-files/IGVFFI7172AMPH/), [IGVFFI9098EJGL](/sequence-files/IGVFFI9098EJGL/), [IGVFFI9160JPFJ](/sequence-files/IGVFFI9160JPFJ/), [IGVFFI7922MDZC](/sequence-files/IGVFFI7922MDZC/), [IGVFFI0612CNEB](/sequence-files/IGVFFI0612CNEB/), [IGVFFI7354VXKL](/sequence-files/IGVFFI7354VXKL/), [IGVFFI1578XZVS](/sequence-files/IGVFFI1578XZVS/), [IGVFFI7331MKFX](/sequence-files/IGVFFI7331MKFX/), [IGVFFI5598LNFE](/sequence-files/IGVFFI5598LNFE/), [IGVFFI5961PXUV](/sequence-files/IGVFFI5961PXUV/), [IGVFFI3011PPJO](/sequence-files/IGVFFI3011PPJO/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS0925RKIM/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0925RKIM](/auxiliary-sets/IGVFDS0925RKIM/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"path": "/auxiliary-sets/IGVFDS0925RKIM/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0925RKIM/",
"accession": "IGVFDS0925RKIM",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-BinC_AmpliconSequencing_AuxiliarySet"
],
"file_set_type": "variant sequencing"
}
],
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:22.459158+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/IGVFDS5031MNRR/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
"preferred_assay_title": "Variant FlowFISH",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"release_timestamp": "2023-12-20T23:07:08.106709+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1488CZUU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1488CZUU",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-BinC"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2374NXLW/",
"accession": "IGVFDS2374NXLW",
"file_set_type": "guide library",
"summary": "Guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "released",
"summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 51-75% expression of PPIF) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "21",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T23:08:20.999272+00:00",
"summary": "Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"symbol": "PPIF",
"synonyms": [
"rotamase F",
"CYP3",
"cyclophilin F",
"mitochondrial cyclophilin",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"CypD",
"Cyp-D",
"cyclophilin 3",
"cyclophilin D",
"CyP-M",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIase F"
]
}
],
"uuid": "2749a5ff-b97a-4027-b78f-8794183e92b4"
}